Research workbench
Crystal structure of the staphylococcal serine protease spla in complex with a specific phosphonate inhibitor
Analyse Crystal structure of the staphylococcal serine protease spla in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MVN
- Type
- protein
- Length
- 793 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine protease spla
- EC
- 3.4.21.-
- UniProt
- Q2FXC2
- Ligands
- I1S
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine protease spla (EC 3.4.21.-) | protein | 198 | 15% helix, 38% strand | Q2FXC2 |
| B | Serine protease spla (EC 3.4.21.-) | protein | 199 | 12% helix, 41% strand | Q2FXC2 |
| C | Serine protease spla (EC 3.4.21.-) | protein | 196 | 12% helix, 42% strand | Q2FXC2 |
| D | Serine protease spla (EC 3.4.21.-) | protein | 200 | 15% helix, 39% strand | Q2FXC2 |
Ligands and binding sites
- I1S · [(1S)-1-{[(benzyloxy)carbonyl]amino}-2-phenylethyl]phosphonic acid · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 546 | 0.81 | 0.87 | 79 | I1S |
| 2 | 184 | 0.61 | 0.82 | 27 | empty |
| 3 | 117 | 0.58 | 0.85 | 33 | I1S |
| 4 | 97 | 0.51 | 0.83 | 28 | I1S |
Interfaces
5 interfaces between chains.
- A–B · 795 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 411 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 365 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 257 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 255 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4MVN · Crystal structure of the staphylococcal serine protease SplA in complex with a specific… · the same entry in another collection · chain D against D, TM-score 1.00
- Q2FXC2 · AlphaFold monomer V2.0 prediction for serine protease spla (Q2FXC2) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q2FXC2
- Elsewhere: RCSB PDB 4MVN · PDBe 4MVN · UniProt Q2FXC2
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